From 092fa2a6da155c93898c8581a1bc6de7c72a9827 Mon Sep 17 00:00:00 2001
From: VarunAnanth2003 <varunananth1@gmail.com>
Date: Sun, 3 Nov 2024 12:45:35 -0800
Subject: [PATCH] line length fixes

---
 casanovo/casanovo.py     | 5 +++--
 casanovo/denovo/model.py | 4 ++--
 tests/conftest.py        | 8 ++++++--
 3 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/casanovo/casanovo.py b/casanovo/casanovo.py
index 5547a807..01098255 100644
--- a/casanovo/casanovo.py
+++ b/casanovo/casanovo.py
@@ -62,8 +62,9 @@ def __init__(self, *args, **kwargs) -> None:
             click.Option(
                 ("-m", "--model"),
                 help="""
-                Either the model weights (.ckpt file) or a URL pointing to the model weights
-                file. If not provided, Casanovo will try to download the latest release automatically.
+                Either the model weights (.ckpt file) or a URL pointing to 
+                the model weights file. If not provided, 
+                Casanovo will try to download the latest release automatically.
                 """,
             ),
             click.Option(
diff --git a/casanovo/denovo/model.py b/casanovo/denovo/model.py
index 40d0cc3d..5e807153 100644
--- a/casanovo/denovo/model.py
+++ b/casanovo/denovo/model.py
@@ -1021,8 +1021,8 @@ def predict_step(self, batch, *args):
         predictions: List[Tuple[List[str], int, float, str, np.ndarray, np.ndarray, str]]
             Model predictions for the given batch of spectra containing spectrum
             ids, precursor charge and m/z, candidate peptide sequences, peptide
-            scores, amino acid-level scores, and associated proteins. Stored separately by
-            spectrum id.
+            scores, amino acid-level scores, and associated proteins.
+            Stored separately by spectrum id.
         """
         store_dict = collections.defaultdict(list)
         for start_idx in range(0, len(batch[0]), self.psm_batch_size):
diff --git a/tests/conftest.py b/tests/conftest.py
index 1729dcb3..009c0737 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -22,14 +22,18 @@ def tiny_fasta_file(tmp_path):
     fasta_file = tmp_path / "tiny_fasta.fasta"
     with fasta_file.open("w+") as fasta_ref:
         fasta_ref.write(
-            ">foo\nMEAPAQLLFLLLLWLPDTTREIVMTQSPPTLSLSPGERVTLSCRASQSVSSSYLTWYQQKPGQAPRLLIYGASTRATSIPARFSGSGSGTDFTLTISSLQPEDFAVYYCQQDYNLP"
+            (
+                ">foo\nMEAPAQLLFLLLLWLPDTTREIVMTQSPPTLSLSPGERVTLSCRASQSVSSSYLTWYQ"
+                "QKPGQAPRLLIYGASTRATSIPARFSGSGSGTDFTLTISSLQPEDFAVYYCQQDYNLP"
+            )
         )
     return fasta_file
 
 
 @pytest.fixture
 def mgf_medium(tmp_path):
-    """An MGF file with 7 spectra and scan numbers, C+57.021 mass modification considered"""
+    """An MGF file with 7 spectra and scan numbers,
+    C+57.021 mass modification considered"""
     peptides = [
         "ATSIPAR",
         "VTLSCR",